Pathway databases overview

Paley SM, Karp PD. The Pathway Tools cellular overview diagram and Omics Viewer. Nucleic Acids Res. 2006 34 3771-3778. Green ML, Karp PD. A Bayesian method for identifying missing enzymes in predicted metabolic pathway databases. BMC Bioinformat. 2004 5 76. 

The World Wide Web has transformed the way in which we obtain and analyze published information on proteins. What only a few years ago would take days or weeks and require the use of expensive computer workstations can now be achieved in a few minutes or hours using personal computers, both PCs and Macintosh, connected to the internet. The Web contains hundreds of sites of Interest to molecular biologists, many of which are listed in Pedro s BioMolecular Research Tools (http // www.fmi.ch/biology/research tools.html). Many sites provide free access to databases that make it very easy to obtain information on structurally related proteins, the amino acid sequences of homologous proteins, relevant literature references, medical information and metabolic pathways. This development has opened up new opportunities for even non-specialists to view and manipulate a structure of interest or to carry out amino-acid sequence comparisons, and one can now rapidly obtain an overview of a particular area of molecular biology. We shall here describe some Web sites that are of interest from a structural point of view. Updated links to these sites can be found in the Introduction to Protein Structure Web site (http // WWW.ProteinStructure.com/). 

Microarray DB Keio University Tool for mapping transcriptome data onto KEGG pathways and for creating a Web-based database with an overview of the entire pathway (http // www.g-language.org/data/marray/)... 

Coenzyme A (CoA) is a cofactor that has been estimated to be used by about 4% of all enzymes, although more recent analysis of the BRENDA database (http //www.brenda.uni-koeln.de/) suggests the number may be closer to 9% (1). The biochemical pathways and processes involving CoA thioesters are diverse and widespread, whereas the kinds of reactions involved primarily follow the inherent reactivity of the thioester functionality. This article provides a brief overview of CoA biosynthesis and a summary of the common types of reactions of CoA thioesters. Also presented is a brief introduction to structural studies and a more extensive description of some types of analogs of natural CoA thioesters that have been employed as mechanistic probes for CoA using enzymes. The application of CoA derivatives and CoA biosynthetic enzymes for the tagging of carrier proteins and carrier protein fusions is also described. 

A database search yields more than 20 000 references that contain Z-E isomerization, cis-trans isomerization, or geometric isomerization as keywords, and the general tendency is an increase in the number of papers devoted to the kinetic aspects of cis-trans isomerization (CTI) in all fields. The main isomerization pathways have probably been discovered, though many remain the object of intense theoretical (see Chapter 7) and experimental research (see Chapters 4—6, 8-10, 13, and 14). In the present chapter, general CTI mechanisms will be divided into homolytic and heterolytic cleavage of the 7r-bond which allows isomerization, though some molecular motifs such as amides are able to switch from cis to trans via both processes. An overview of CTI in metal complex (mainly thermal, photochemical, and oxidative isomerizations) will be the purpose of Chapter 14 and will not be detailed here. 

Reaction pathway synthesis delivers the basis for a chemical process. The methods employed vary from databases to heuristic and inductive techniques. Almost all researchers focus on the production of organic compounds. The paper by Mavrovounitis gives a good overview on this research area called Computer Aided Organic Synthesis. ... 

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